Publications

Preprints

Kos J.T., Safonova Y., Shields K.M., Silver C.A., Lees W.D., Collins A.M. and C.T. Watson. Characterization of Extensive Diversity In Immunoglobulin Light Chain Variable Germline Genes Across Biomedically Important Mouse Strains. bioRxiv doi: https://doi.org/10.1101/2022.05.01.489089

Mikelov A, Nefediev G, Tashkeev A, Rodriguez OL, Ortmans DA, Skatova V, Izraelson M, Davydov A, Poslavsky S, Rahmouni S, Watson CT, Chudakov D, Boyd SD, Bolotin D. Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR. doi: 10.1101/2023.10.10.561703.

DongAhn Yoo, Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, Steven J. Solar, Dmitry Antipov, Brandon D. Pickett, Yana Safonova, Francesco Montinaro, Yanting Luo, Joanna Malukiewicz, Jessica M. Storer, Jiadong Lin, Abigail N. Sequeira, Riley J. Mangan, Glenn Hickey, Graciela Monfort Anez, Parithi Balachandran, Anton Bankevich, Christine R. Beck, Arjun Biddanda, Matthew Borchers, Gerard G. Bouffard, Emry Brannan, Shelise Y. Brooks, Lucia Carbone, Laura Carrel, Agnes P. Chan, Juyun Crawford, Mark Diekhans, Eric Engelbrecht, Cedric Feschotte, Giulio Formenti, Gage H. Garcia, Luciana de Gennaro, David Gilbert, Richard E. Green, Andrea Guarracino, Ishaan Gupta, Diana Haddad, Junmin Han, Robert S. Harris, Gabrielle A. Hartley, William T. Harvey, Michael Hiller, Kendra Hoekzema, Marlys L. Houck, Hyeonsoo Jeong, Kaivan Kamali, Manolis Kellis, Bryce Kille, Chul Lee, Youngho Lee, William Lees, Alexandra P. Lewis, Qiuhui Li, Mark Loftus, Yong Hwee Eddie Loh, Hailey Loucks, Jian Ma, Yafei Mao, Juan F. I. Martinez, Patrick Masterson, Rajiv C. McCoy, Barbara McGrath, Sean McKinney, Britta S. Meyer, Karen H. Miga, Saswat K. Mohanty, Katherine M. Munson, Karol Pal, Matt Pennell, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Francisca R. Ringeling, Joana L. Rocha, Oliver A. Ryder, Samuel Sacco, Swati Saha, Takayo Sasaki, Michael C. Schatz, Nicholas J. Schork, Cole Shanks, Linnéa Smeds, Dongmin R. Son, Cynthia Steiner, Alexander P. Sweeten, Michael G. Tassia, Françoise Thibaud-Nissen, Edmundo Torres-González, Mihir Trivedi, Wenjie Wei, Julie Wertz, Muyu Yang, Panpan Zhang, Shilong Zhang, Yang Zhang, Zhenmiao Zhang, Sarah A. Zhao, Yixin Zhu, Erich D. Jarvis, Jennifer L. Gerton, Iker Rivas-González, Benedict Paten, Zachary A. Szpiech, Christian D. Huber, Tobias L. Lenz, Miriam K. Konkel, Soojin V. Yi, Stefan Canzar, Corey T. Watson, Peter H. Sudmant, Erin Molloy, Erik Garrison, Craig B. Lowe, Mario Ventura, Rachel J. O’Neill, Sergey Koren, Kateryna D. Makova, Adam M. Phillippy, Evan E. Complete sequencing of ape genomes. Eichler. https://www.biorxiv.org/content/10.1101/2024.07.31.605654v1

Zhu Y., Watson C.T., Safonova Y., Pennell M., and A. Bankevich. Assessing Assembly Errors in Immunoglobulin Loci: A Comprehensive Evaluation of Long-read Genome Assemblies Across Vertebrates. https://www.biorxiv.org/content/10.1101/2024.07.19.604360v2

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2024

Theodore S. Kalbfleisch, Stephanie D. McKay, Brenda M. Murdoch, David L. Adelson, Diego Almansa-Villa...[]...Corey Watson, Rosemarie Weikard, Klaus Wimmers, Shangqian Xie, Liu Yang, Timothy P. L. Smith, Rachel J. O’Neill & Benjamin D. Rosen. 2024. The Ruminant Telomere-to-Telomere (RT2T) Consortium. Nature Genetics. https://doi.org/10.1038/s41588-024-01835-2

Engelbrecht E., Rodriguez O.L., and C.T. Watson. 2024. Addressing technical pitfalls in pursuit of molecular factors that mediate immunoglobulin gene regulation. In press, Journal of Immunology. https://doi.org/10.4049/jimmunol.2400131

Engelbrecht E., Rodriguez O.L., Shields K., Schultze S., Tieri D., Jana U., Yaari G., Lees W., Smith M.L. and C.T. Watson. 2024. Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry. Genes and Immunity. https://www.nature.com/articles/s41435-024-00279-2

Schiffner T., Phung I., Ray R., Irimia A., Tian M., Swanson O., Lee J-H, Lee C-C.D., Marina-Zárate E, Cho S.Y., Huang J., Ozorowski G., Skog P.D., Serra A.M., Rantalainen K., Allen J.D., Baboo S, Rodriguez O.L., Himansu S., Zhou J., Hurtado J., Flynn C.T., McKenney K., Havenar-Daughton C., Saha S., Shields K., Schultze S., Smith M.L., Liang C-H., Toy L., Pecetta S., Lin Y-C, Willis J.R., Sesterhenn F., Kulp D.W., Hu X., Cottrell C.A., Zhou X., Ruiz J., Wang X., Nair U., Kirsch K.A., Cheng H-J., Davis J., Kalyuzhniy O., Liguori A., Diedrich J.K., Ngo J.T., Lewis V., Phelps N., Tingle R.D., Spencer S., Georgeson E., Adachi Y., Kubitz M., Eskandarzadeh S., Elsliger M.A., Amara R.R., Landais E., Briney B., Burton D.R., Carnathan D.G., Silvestri G., Watson C.T., Yates III J.R., Paulson J.C., Crispin M., Grigoryan G., Ward A.B., Sok D., Alt F.W., Wilson I.A., Batista F.D., Crotty S. and W.R. Schief. 2024. Vaccination induces broadly neutralizing antibody precursors to HIV gp41. Nature Immunology. doi: 10.1038/s41590-024-01833-w

Steichen J.M., Phung I., Salcedo E., Ozorowski G., Willis J.R., Baboo S., Liguori A., Cottrell C.A., Torres J.L., Madden P.J., Ma K.M., Sutton H.J., Lee J.H., Kalyuzhniy O., Allen J.D., Rodriguez O.L., Adachi Y., Mullen T.M., Georgeson E., Kubitz M., Burns A., Barman S., Mopuri R., Metz A., Altheide T.K., Diedrich J.K., Saha S., Shields K., Schultze S.E., Smith M.L., Schiffner T., Burton D.R., Watson C.T., Bosinger S.E., Crispin M., Yates J.R. 3rd, Paulson J.C., Ward A.B., Sok D., Crotty S. and W.R. Schief. 2024. Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates. Science. 384(6697):eadj8321.

Lees W., Saha S., Yaari G. and C.T. Watson. 2024. Digger: Directed annotation of immunoglobulin and T cell receptor V, D and J gene sequences and assemblies. Bioinformatics https://doi.org/10.1093/bioinformatics/btae144

Collins A.M., Ohlin M., Corcoran M., Heather J.M., Ralph D., Law M., Martínez-Barnetche J., Ye J., Richardson E., Gibson W.S., Rodriguez O.L., Peres A., Yaari G., Watson C.T. and W.D. Lees. 2024. AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes. Front Immunol. Volume 14. https://doi.org/10.3389/fimmu.2023.1330153

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2023

Peres A., Lees W.D., Rodriguez O.L., Lee N.Y., Polak P., Hope R., Kedmi M., Collins A.M., Ohlin M., Kleinstein S.K., Watson C.T. and G. Yaari. IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data. Nucleic Acids Res. https://doi.org/10.1093/nar/gkad603

Rodriguez O.L., Safonova Y., Silver C.A., Shields K., Gibson W.S., Kos J.T., Tieri D., Ke H., Jackson K.J.L, Boyd S.D., Smith M.L., Marasco W.A., and C.T. Watson. Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire. Nat Commun 14, 4419

Ford E.E., Tieri D., Rodriguez O.L., Francoeur N.J., Soto J., Kos J.T., Peres A., Gibson W., Silver C.A., Deikus G., Hudson E., Woolley C.R., Beckmann N., Charney A., Mitchell T.C., Yaari G., Sebra R.P., Watson C.T.* and M.L. Smith*. 2023 FLAIRR-seq: A novel method for single molecule sequencing of near full-length immunoglobulin heavy chain repertoires. J Immunol. ji2200825.

Lees W.D., Christley S., Peres A., Kos J.T., Corrie B., Ralph D., Breden F., Cowell L.G., Yaari G., Corcoran M., Hedestam G.B.K., Ohlin M., Collins A.M., Watson C.T., Busse C.E., and The AIRR Community. 2023. AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets. Immunoinformatics. 10:100025

Nickerson K.M., Smita S., Hoehn K.B., Marinov A.D., Thomas K.B., Kos J.T., Yang Y., Bastacky S.I., Watson C.T., Kleinstein S.H. and M.J. Shlomchik. 2023. Age-Associated B Cells are Heterogenous and Dynamic Drivers of Autoimmunity. J Exp Med. 220(5):e20221346.

Pennell M., Rodriguez O.L., Watson C.T. and V. Greiff. 2023. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol. 44(1):7-21. doi: 10.1016/j.it.2022.11.001.

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2022

Rodriguez O.L., Silver C.A., Shields K., Smith M.L. and C.T. Watson. 2022. Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta and beta loci. Cell Genomics. https://doi.org/10.1016/j.xgen.2022.100228

Gibson W.S., Rodriguez O.L., Shields K., Silver C.A., Dorgham A., Emery M., Deikus G., Sebra R., Eichler E.E., Bashir A., Smith M.L., and C.T. Watson. 2022. Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation. Genes and Immunity. doi: 10.1038/s41435-022-00188-2

Fichtner M.L., Hoehn K.B., Ford E.E., Mane-Damas M., Oh S., Waters P., Payne A.S., Smith M.L., Watson C.T., Losen M., Martinez-Martinez P., Nowak R.J., Kleinstein S.H. and K.C. O'Connor. 2022. Reemergence of pathogenic, autoantibody-producing B cell clones in myasthenia gravis following B cell depletion therapy. Acta Neuropathol Commun. 10(1):154.

Ford M., Hari A., Rodriguez O.L., Xu J., Lack J., Oguz C., Zhang Y., Weber S., Magglioco M., Barnett J., Xirasagar S., Samuel S., Imberti L., Bonfanti P., Biondi A., Dalgard C.L., Chanock S., Rosen L., Holland S., Su H., Notarangelo L., NIAID COVID Consortium, Vishkin U., Watson C.T., and S.C. Sahinalp. 2022. ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data. Cell Syst. 13(10):808-816.e5.

Collins A.M., Watson C.T., and F. Breden. 2022. Immunoglobulin genes, reproductive isolation and vertebrate speciation. Immunol Cell Biol. 100(7):497-506.

Babrak L., Marquez S., Busse C.E., Lees W.D., Miho E., Ohlin M., Rosenfeld A.M., Stervbo U., Watson C.T. and C.A. Schramm; AIRR Community. 2022. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation. Methods Mol Biol. 2453:279-296

Jackson KJL, Kos J.T., Lees W., Gibson W.S., Smith M.L., Peres A., Yaari G., Corcoran M., Busse C.E., Ohlin M., Watson C.T. and A.M. Collins. 2022. A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice. Front Immunol. 13:888555

Safonova Y., Shin S.B., Kramer L., Reecy J., Watson C.T., Smith T.P.L., and P.A. Pevzner. 2022. Revealing how variations in antibody repertoires correlate with vaccine responses. Genome Res. 2022 Apr;32(4):791-804.

Geller A., Shrestha R., Woeste M., Guo H., Hu X., Ding C., Andreeva K., Chariker J., Zhou M., Tieri D., Watson C.T., Mitchell R., Zhang H., Li Y., Martin R., Rouchka R., and J. Yan. 2022. The Induction of Peripheral Trained Immunity in the Pancreas Incites Anti-tumor Activity to Control Pancreatic Cancer Progression. Nat Commun. 13(1):759. doi: 10.1038/s41467-022-28407-4.

Omer A., Peres A., Rodriguez O.L., Watson C.T., Lees W., Polak P., Collins A.M., G. Yaari. 2022. T Cell Receptor Beta (TRB) Germline Variability is Revealed by Inference From Repertoire Data. Genome Med. 14(1):2. doi: 10.1186/s13073-021-01008-4.

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2021

Rodriguez O.L., Sharp A.J., and C.T. Watson. 2021. Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci. PLoS One. 16(12):e0261374

Zhou M, Dascani P, Ding C, Kos JT, Tieri D, Lin X, Caster D, Powell D, Wen C, Watson CT, Yan J. 2021. Integrin CD11b Negatively Regulates B Cell Receptor Signaling to Shape Humoral Response during Immunization and Autoimmunity. J Immunol. 207(7):1785-1797.

Morrissey S.M., Zhang F., Yang C., Wang Z., Hu X., Fox M., Ding C, Zhang H., Guo H., Tieri D., Kong M., Watson C.T., Mitchell R., Huang J. and J. Yan. 2021. Tumor-derived exosomes drive immunosuppressive macrophages in a pre-metastatic niche through glycolytic dominant metabolic reprogramming. Cell Metab. 17:S1550-4131(21)00421-6

Lee J.H., Toy L., Kos J.T., Safonova Y., Fung K., Greenbaum J., Schief W.R., Havenar-Daughton C., Watson C.T.* and S. Crotty*. 2021. Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells.

Peng K., Safonova Y., Shugay M., Popejoy A., Rodriguez O.L., Breden F., Brodin P., Burkhardt A.M., Bustamante C., Cao-Lormeau V-M., Corcoran M.M., Duffy D., Fuentes-Guajardo M., Fujita R., Greiff V., Jonsson V.D., Liu X., Quintana-Murci L., Rossetti M., Xie J., Yaari G., Zhang W., Abedalthagafi M.S., Adekoya K.O., Ahmed R.A., Chang W., Gray C., NakamuraLees Y., W.D., Khatri P., Alachkar H.*, Scheepers C.*, Watson C.T.*, Karlsson Hedestam G.B.* and S, Mangul*. 2021. Diversity in immunogenomics: the value and the challenge. Nat Methods. 18(6):588-591

Kenter A.L.*, Watson C.T.* and J-H. Spille*. 2021. Igh Locus Polymorphism May Dictate Topological Chromatin Conformation and V Gene Usage in the Ig Repertoire. Front. Immunol. https://doi.org/10.3389/fimmu.2021.682589

Morrissey S.M., Geller A.E., Hu X., Tieri D., Cooke E.A., Ding C., Klaes C.K., Cooke E.A., Woeste M., Martin Z.C., Chen O., Bush S.E., Zhange H., Cavallazi R., Clifford S.P., Chen J., Ghare S., Barve S.S., Cai L., Kong M., Rouchka E.C., McLeish K.R., Uriarte S.M., Watson C.T., Huang J. and J. Yan. 2021. A specific low-density neutrophil population correlates with hypercoagulation and disease severity in hospitalized COVID-19 patients. JCI Insight. 10.1172/jci.insight.148435

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2020

Collins A.M., Yaari G., Shepherd A.J., Lees W. and C.T. Watson. 2020. Germline immunoglobulin genes: disease susceptibility genes hidden in plain sight? Curr Opin Syst Biol. (In press)

Rodriguez O.L., Gibson W.S., Parks T., Emery M., Powell J., Strahl M., Deikus G., Auckland K., Eichler E.E., Marasco W.A., Sebra R., Sharp A.J., Smith M.L., Bashir A. and C.T. Watson. 2020. A novel framework for characterizing genomic haplotype diversity in the human immunoglobulin heavy chain locus. Front Immunol. (In press)

Alsoussi W.B., Turner J.S., Case J.B., Zhao H., Schmitz A.J., Zhou J.Q., Chen R.E., Lei T., Rizk A.A., McIntire K.M., Winkler E.S., Fox J.M., Kafai N.M., Thackray L.B., Hassan A.O., Amanat F., Krammer F., Watson C.T., Kleinstein S.H., Fremont D.H., Diamond M.S. and A.H. Ellebedy. 2020. A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection. J Immunol. (In press)

Christley S., Aguiar A., Blanck G., Breden F., Bukhari S.A.C., Busse C.E., Jaglale J., Harikrishnan S.L., Laserson U., Peters B., Rocha A., Schramm C.A., Taylor S., Vander Heiden J.A., Zimonja B., The AIRR Community, Watson C.T., Corrie B. and L.G. Cowell. 2020. The ADC API: a web API for the programmatic query of the AIRR Data Commons. Front Immunol. (In press)

Ford M., Haghshenas E., Watson C.T. and S.C. Sahinalp. 2020. Genotyping and Copy Number Analysis of Immunoglobin Heavy Chain Variable Genes using Long Reads. iScience. (In press)

Snyder K. E., Pittard C.M., Fowler A. and C.T. Watson. 2020. “Epic-Genetics”: An exploration of pre-service helping professionals’ (mis)understanding of epigenetic influences on human development. Teaching & Learning Inquiry. 8(1):122-137

Do A., Watson C.T., Cohain A., Griffin R., Grishin A., Wood R., Burks A.W., Jones S., Scurlock A., Leung D., Sampson H., Sicherer S., Sharp A.J., Schadt E. and S. Bunyavanich. 2020. Dual transcriptomic and epigenomic study of reaction severity in peanut allergic children. J Allergy Clin Immunol. 145(4):1219-1230

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2019

Busse C.E., Jackson K.J.L., Watson C.T. and A.M. Collins. 2019. A proposed new nomenclature for the immunoglobulin genes of Mus musculus. Front Immunol. 10:2961

Omer A., Shemesh O., Peres A., Polak P., Shepherd A.J., Watson C.T., Boyd S.D., Collins A.M., Lees W. and G. Yaari. 2019. VDJbase: an adaptive immune receptor genotype and haplotype database. Nucleic Acids Res. 48(D1):D1051-D1056

Lees W., Busse C.E., Corcoran M., Ohlin M., Scheepers C., Matsen F.A., Yaari G., Watson C.T., The AIRR Community, Collins A. and A.J. Shepherd. 2019. OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Res. 48(D1):D964-D970

Watson C.T., Kos J.T., Gibson W.S., Busse C.E., Newman L., Deikus G., Smith M.L., Jackson K.J.L. and A.M. Collins. 2019. A comparison of immunoglobulin IGHV, IGHD and IGHJ genes in wild‐derived and classical inbred mouse strains. Immunol Cell Biol. 97:888-901

Cirelli K.M., Carnathan D.G., Nogal B., Rodriguez O.L., Martin J.T., Upadhyay A.U., Enemuo C.A., Gebru E.H., Choe Y., Viviano F., Nakao C., Pauthner M., Menis S., Reiss S., Cottrell C.A., Smith M.L., Bastidas R., Gibson W., Wolabaugh A.N., Melo A.B., Cosette B., Kuman V., Patel N., Tokatlian T., Menis S., Kulp D.W., Burton D.R., Murrell B., Bosinger S.E., Schief W.R., Ward A.B., Watson C.T., Silvestri G., Irvine D.J. and S. Crotty. 2019. Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. Cell. 177(5):1153-1171.e28.

Castro K., Ntranos A., Amatruda M., Petracca M., Kosa P., Chen E.Y., Morstein J., Trauner D., Watson C.T., Kiebish M.A., Bielekovad B., Inglese M., Sand I.K. and P. Casaccia. 2019. Body Mass Index in Multiple Sclerosis modulates ceramide-induced DNA methylation and disease course. Ebiomedicine. 43:392-410

Hardesty J.E., Wahlang B., Falkner K.C., Shi H., Jin J., Zhou Y., Wilkey D.W., Merchant M., Watson C.T., Feng W., Morris A., Hennig B., Prough R.A. and M.C. Cave. 2019. Proteomic analysis reveals novel mechanisms by which polychlorinated biphenyls compromise the liver promoting diet-induced steatohepatitis. J. Proteome Res. 18(4):1582-1594

Ohlin M., Scheepers C., Corcoran M., Lees W.D., Busse C.E., Bagnara D., Thörnqvist L., Bürckert J.P., Jackson K.J.L., Ralph D., Schramm C., Marthandan N., Breden F., Scott J.K., Matsen E., Greiff V., Yaari G., Kleinstein S.H., Christley S., Sherkow J.S., Kossida S., Lefranc M.P., van Zelm M.C., Watson C.T., and A.M. Collins. 2019. Inferred allelic variants of immunoglobulin receptor genes: a system for their evaluation and documentation. Front Immunol. 10:435

Ntranos A., Ntranos V., He Y., Bonnefil V., Liu J., Kim-Schulze S., He Y., Zhu Y., Brandstadter R., Watson C.T., Sharp A.J., Katz-Sand I. and P. Casaccia. 2019. Fumarates target the metabolic-epigenetic interplay of brain-homing T cells in multiple sclerosis. Brain. 142(3):647-661

Gadala-Maria D., Gidoni M., Marquez S., Vander Heiden J.A., Kos J.T., Watson C.T., O’Connor K.C., Yaari G. and S.H. Kleinstein. 2019. Identification of subject-specific immunoglobulin alleles from expressed repertoire sequencing data. Front Immunol. 10:129

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2018
Hardesty J.E., Wahlang B., Falkner K.C., Shi H., Jin J., Wilkey D., Merchant M., Watson C.T., Prough R.A. and M.C.Cave. 2018. Hepatic signalling disruption by pollutant Polychlorinated biphenyls in steatohepatitis. Cellular Signaling. 18(4):1582-1594

Garg P., Joshi R., Watson C.T., and A.J. Sharp. 2018. A survey of DNA methylation polymorphism in the human genome identifies environmentally responsive co-regulated networks of epigenetic variation. PLoS Genet. 14(10):e1007707

Collins A.M. and C.T. Watson. 2018. Immunoglobulin light chain gene rearrangements, receptor editing and the development of a self-tolerant antibody repertoire. Front Immunol. 9:2249.

Cobb C., Watson C.T., and S.R. Ellis. 2018. Establishing Best Practices for Effective Online Learning Modules: a Single Institution Study. Med Sci Educ. 28:683–691

Barbosa M., Joshi R.S., Garg P., Martin-Trujillo A., Patel N., Jadhav B., Watson C.T., Gibson W., Chetnik K., Tessereau C., Mei H., De Rubeis S., Reichert J., Lopes F., Vissers L.E.L.M., Kleefstra T., Grice D.E., Edelmann L., Soares G., Maciel P., Brunner H.G., Buxbaum J.D., Gelb B.D., and A.J. Sharp. 2018. Identification of rare de novo epigenetic variations in congenital disorders. Nat Commun. 9(1):2064

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2017

Breden F. and C.T. Watson. 2017. Using High-Throughput Sequencing to Characterize the Development of the Antibody Repertoire During Infections: A Case Study of HIV-1. In: Lim T. (eds) Recombinant Antibodies for Infectious Diseases. Adv Exp Med Biol. 1053:245-263. Springer, Cham

Watson C.T.*, Cohain A.T.*, Griffin R.S., Chun Y., Grishin A., Hacyznska H., Hoffman G.E., Beckmann N.D., Shah H., Dawson P., Henning A., Wood R., Burks A.W., Jones S.M., Leung D. Y.M., Sicherer S., Sampson H.A., Sharp A.J., Schadt E.E., and S. Bunyavanich. 2017. Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions. NatCommun. 8(1):1943 *Co-first authors

Rubelt F., Busse C.E., Bukhari S.A.C., Bürckert J-P., Mariotti-Ferrandiz E., Cowell L., Watson C.T., Marthandan N., Faison W.J., Hershberg U., Laserson U., Corrie B., Davis M.M., Peters B., Lefranc M-P., Scott J.K., Breden F., The AIRR Community, Luning Prak E.L. and S.H. Kleinstein. 2017. AIRR Community Recommendations for Sharing Immune Repertoire Sequencing Data. Nat Immunol. 18(12):1274-1278

Sandkam B.A., Joy J.B., Watson C.T. and F. Breden. 2017. Genomic environment impacts color vision evolution in a family with visually-based sexual selection. Genome Biol Evol. 9(11):3100-3107

Breden F., Luning Prak E.T., Peters B., Rubelt F., Schramm C.A., Busse C., Vander Heiden J.A., Christley S., Bukhari S.A., Thorogood A., Matsen F., Wine Y., Laserson U., Klatzmann D., Douek D., Lefranc M-P., Collins A.M., Bubela T., Kleinstein S.H., Watson C.T., Cowell L.G., Scott J.K., and T.B. Kepler. 2017. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol. 8:1418

Watson C.T.*, Glanville J.*, and W.A. Marasco*. 2017. The Individual and Population Genetics of Antibody Immunity. Trends Immunol. 38(7):459-470 *Corresponding

Watson C.T.*, Matsen IV F.A., Jackson K.J.L., Bashir A., Smith M.L., Glanville J., Breden F., Kleinstein S.H., Collins A.M., and C.E. Busse*. 2017. Comment on "A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data". J Immunol. 198:3371-3373 *Corresponding